Promoter or enhancer, what’s the difference? Deconstruction of established distinctions and presentation of a unifying model

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

An integrated map of genetic variation from 1,092 human genomes

The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works

High-Resolution Profiling of Histone Methylations in the Human Genome

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · see citing works

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302 · see citing works

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716 · see citing works

The Role of Chromatin during Transcription

Li, B., Carey, M., & Workman, J. L. (2007) · Cell · doi:10.1016/j.cell.2007.01.015 · Cited by 3,503 · see citing works

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 3× · see citing works

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works

The accessible chromatin landscape of the human genome

Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679 · see citing works

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533 · see citing works

Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450 · see citing works

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works

Transcription factors: from enhancer binding to developmental control

Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227 · see citing works

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033 · see citing works

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986 · see citing works

Mediator and cohesin connect gene expression and chromatin architecture

Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939 · see citing works

Genome-Wide Location and Function of DNA Binding Proteins

Ren, B., Robert, F., Wyrick, J. J., Aparicio, O. M., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N. M., Kanin, E. I., et al. (2000) · Science · doi:10.1126/science.290.5500.2306 · Cited by 1,768 · see citing works

Expression of a β-globin gene is enhanced by remote SV40 DNA sequences

Banerji, J., Rusconi, S., & Schaffner, W. (1981) · Cell · doi:10.1016/0092-8674(81)90413-x · Cited by 1,724 · see citing works

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639 · see citing works

Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse

Bernstein, B., Kamal, M., Lindblad‐Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., McMahon, S., Karlsson, E. K., Kulbokas, E. J., Gingeras, T., et al. (2005) · Cell · doi:10.1016/j.cell.2005.01.001 · Cited by 1,509 · see citing works

The long-range interaction landscape of gene promoters

Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008) · Cell · doi:10.1016/j.cell.2007.12.014 · Cited by 1,415 · see citing works

A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes

Banerji, J., Olson, L., & Schaffner, W. (1983) · Cell · doi:10.1016/0092-8674(83)90015-6 · Cited by 1,407 · see citing works

A map of the cis-regulatory sequences in the mouse genome

Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361 · see citing works

Transcriptional enhancers: from properties to genome-wide predictions

Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356 · see citing works

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.014 · Cited by 1,232 · see citing works

A high-resolution map of the three-dimensional chromatin interactome in human cells

Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works

Applied bioinformatics for the identification of regulatory elements

Wasserman, W. W., & Sandelin, A. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1315 · Cited by 1,206 · see citing works

In vivo enhancer analysis of human conserved non-coding sequences

Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125 · see citing works

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

Li, W., Notani, D., Ma, Q., Tanasa, B., Nunez, E., Chen, A. Y., Merkurjev, D., Zhang, J., Ohgi, K., Song, X., et al. (2013) · Nature · doi:10.1038/nature12210 · Cited by 1,049 · see citing works

Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development

Woolfe, A., Goodson, M., Goode, D. K., Snell, P., McEwen, G. K., Vavouri, T., Smith, S. F., North, P., Callaway, H., Kelly, K., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030007 · Cited by 970 · see citing works

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., Muller, H., Ragoussis, J., Wei, C.-L., & Natoli, G. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000384 · Cited by 934 · see citing works

Enhancer function: new insights into the regulation of tissue-specific gene expression

Ong, C.-T., & Corces, V. G. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2957 · Cited by 929 · see citing works

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

Wang, D., García-Bassets, I., Benner, C. W., Li, W., Su, X. B., Zhou, Y., Qiu, J., Liu, W., Kaikkonen, M. U., Ohgi, K. A., et al. (2011) · Nature · doi:10.1038/nature10006 · Cited by 820 · see citing works

Functional and Mechanistic Diversity of Distal Transcription Enhancers

Bulger, M., & Groudine, M. (2011) · Cell · doi:10.1016/j.cell.2011.01.024 · Cited by 803 · see citing works

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

Rhee, H. S., & Pugh, B. F. (2011) · Cell · doi:10.1016/j.cell.2011.11.013 · Cited by 760 · see citing works

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan, C. G., Kinney, J. B., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2137 · Cited by 711 · see citing works

Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription

Kaikkonen, M. U., Spann, N. J., Heinz, S., Romanoski, C. E., Allison, K. A., Stender, J. D., Chun, H. B., Tough, D. F., Prinjha, R. K., Benner, C., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.07.010 · Cited by 672 · see citing works

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

Berman, B. P., Nibu, Y., Pfeiffer, B. D., Tomančák, P., Celniker, S., Levine, M., Rubin, G. M., & Eisen, M. B. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.231608898 · Cited by 605 · see citing works

Chromatin marks identify critical cell types for fine mapping complex trait variants

Trynka, G., Sandor, C., Han, B., Xu, H., Stranger, B. E., Liu, X. S., & Raychaudhuri, S. (2013) · Nature Genetics · doi:10.1038/ng.2504 · Cited by 580 · see citing works

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

Zentner, G. E., Tesar, P. J., & Scacheri, P. C. (2011) · Genome Research · doi:10.1101/gr.122382.111 · Cited by 564 · see citing works

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

Lam, M. T. Y., Cho, H., Lesch, H. P., Gosselin, D., Heinz, S., Tanaka-Oishi, Y., Benner, C., Kaikkonen, M. U., Kim, A. S., Kosaka, M., et al. (2013) · Nature · doi:10.1038/nature12209 · Cited by 548 · see citing works

Absence of a simple code: how transcription factors read the genome

Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537 · see citing works

Enhancer loops appear stable during development and are associated with paused polymerase

Ghavi-Helm, Y., Klein, F. A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W., & Furlong, E. E. M. (2014) · Nature · doi:10.1038/nature13417 · Cited by 536 · see citing works

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

Lenhard, B., Sandelin, A., & Carninci, P. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3163 · Cited by 513 · see citing works

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

Odom, D. T., Dowell, R. D., Jacobsen, E. S., Gordon, W., Danford, T. W., MacIsaac, K. D., Rolfe, P. A., Conboy, C. M., Gifford, D. K., & Fraenkel, E. (2007) · Nature Genetics · doi:10.1038/ng2047 · Cited by 506 · see citing works

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502 · see citing works

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

Hah, N., Danko, C. G., Core, L. J., Waterfall, J. J., Siepel, A. C., Lis, J. T., & Kraus, W. L. (2011) · Cell · doi:10.1016/j.cell.2011.03.042 · Cited by 488 · see citing works

Looping Back to Leap Forward: Transcription Enters a New Era

Levine, M., Cattoglio, C., & Tjian, R. (2014) · Cell · doi:10.1016/j.cell.2014.02.009 · Cited by 481 · see citing works

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

Li, X., MacArthur, S., Bourgon, R., Nix, D. A., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Hendriks, C. L. L., et al. (2008) · eScholarship (California Digital Library) · doi:10.1371/journal.pbio.0060027 · Cited by 479 · see citing works

Enhancer transcripts mark active estrogen receptor binding sitesPreprint

Hah, N., Murakami, S., Nagari, A., Danko, C. G., & Kraus, W. L. (2013) · Genome Research · doi:10.1101/gr.152306.112 · Cited by 475 · see citing works

Shadow enhancers as a source of evolutionary novelty

Hong, J.-W., Hendrix, D. A., & Levine, M. S. (2008) · Science · doi:10.1126/science.1160631 · Cited by 474 · see citing works

Active chromatin domains are defined by acetylation islands revealed by genome-wide mappingPreprint

Roh, T., Cuddapah, S., & Zhao, K. (2005) · Genes & Development · doi:10.1101/gad.1272505 · Cited by 465 · see citing works

Determinants and dynamics of genome accessibility

Bell, O., Tiwari, V. K., Thomä, N. H., & Schübeler, D. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3017 · Cited by 457 · see citing works

Spatial and Temporal Recruitment of Androgen Receptor and Its Coactivators Involves Chromosomal Looping and Polymerase Tracking

Wang, Q., Carroll, J. S., & Brown, M. A. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.07.018 · Cited by 450 · see citing works

Transcriptional Enhancers in Animal Development and Evolution

Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.06.070 · Cited by 449 · see citing works

Recruitment of CBP/p300 by the IFNβ Enhanceosome Is Required for Synergistic Activation of Transcription

Merika, M., Williams, A. J., Chen, G., Collins, T., & Thanos, D. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80028-3 · Cited by 435 · see citing works

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

Sherwood, R. I., Hashimoto, T., O'Donnell, C. W., Lewis, S., Barkal, A. A., van Hoff, J. P., Karun, V., Jaakkola, T., & Gifford, D. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2798 · Cited by 416 · see citing works

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

Almada, A. E., Wu, X., Kriz, A. J., Burge, C. B., & Sharp, P. A. (2013) · Nature · doi:10.1038/nature12349 · Cited by 406 · see citing works

Combinatorial binding predicts spatio-temporal cis-regulatory activity

Zinzen, R. P., Girardot, C., Gagneur, J., Braun, M. M., & Furlong, E. E. M. (2009) · Nature · doi:10.1038/nature08531 · Cited by 397 · see citing works

The 3D genome in transcriptional regulation and pluripotency

Gorkin, D. U., Leung, D., & Ren, B. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.05.017 · Cited by 391 · see citing works

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

Teytelman, L., Thurtle, D. M., Rine, J., & van Oudenaarden, A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1316064110 · Cited by 389 · see citing works

H3K4 tri‐methylation provides an epigenetic signature of active enhancers

Pękowska, A., Benoukraf, T., Cabeza, J. Z., Belhocine, M., Koch, F., Holota, H., Imbert, J., Andrau, J., Ferrier, P., & Spicuglia, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.295 · Cited by 365 · see citing works

Inducible gene expression: diverse regulatory mechanisms

Weake, V. M., & Workman, J. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2781 · Cited by 365 · see citing works

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

Koch, F., Fenouil, R., Gut, M., Cauchy, P., Albert, T., Cabeza, J. Z., Spicuglia, S., de la Chapelle, A. L., Heidemann, M., Hintermair, C., et al. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2085 · Cited by 333 · see citing works

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

Stergachis, A. B., Neph, S. J., Reynolds, A. P., Humbert, R., Miller, B. G., Paige, S. L., Vernot, B., Cheng, J. B., Thurman, R. E., Sandstrom, R. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.07.020 · Cited by 331 · see citing works

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Kheradpour, P., Ernst, J., Melnikov, A., Rogov, P., Wang, L., Zhang, X., Alston, J., Mikkelsen, T. S., & Kellis, M. (2013) · Genome Research · doi:10.1101/gr.144899.112 · Cited by 315 · see citing works

Regulation of RNA polymerase II activation by histone acetylation in single living cells

Stasevich, T. J., Hayashi‐Takanaka, Y., Sato, Y., Maehara, K., Ohkawa, Y., Sakata-Sogawa, K., Tokunaga, M., Nagase, T., Nozaki, N., McNally, J. G., et al. (2014) · Nature · doi:10.1038/nature13714 · Cited by 287 · see citing works

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

Ntini, E., Järvelin, A. I., Bornholdt, J., Chen, Y., Boyd, M., Jørgensen, M., Andersson, R., Hoof, I., Schein, A., Andersen, P. R., et al. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2640 · Cited by 287 · see citing works

Enhancers as information integration hubs in development: lessons from genomics

Buecker, C., & Wysocka, J. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.02.008 · Cited by 286 · see citing works

Different gene regulation strategies revealed by analysis of binding motifs

Wunderlich, Z., & Mirny, L. A. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.08.003 · Cited by 282 · see citing works

Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content

Houben, A., Demidov, D., Gernand, D., Meister, A., Leach, C. R., & Schubert, I. A. (2003) · The Plant Journal · doi:10.1046/j.1365-313x.2003.01681.x · Cited by 281 · see citing works

Intragenic Enhancers Act as Alternative Promoters

Kowalczyk, M. S., Hughes, J. R., Garrick, D., Lynch, M. D., Sharpe, J. A., Sloane-Stanley, J. A., McGowan, S. J., De Gobbi, M., Hosseini, M., Vernimmen, D., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.021 · Cited by 267 · see citing works

The pluripotent genome in three dimensions is shaped around pluripotency factors

de Wit, E., Bouwman, B. A. M., Zhu, Y. K., Klous, P., Splinter, E., Verstegen, M. J. A. M., Krijger, P. H. L., Festuccia, N., Nora, E. P., Welling, M., et al. (2013) · Nature · doi:10.1038/nature12420 · Cited by 263 · see citing works

Large-scale discovery of enhancers from human heart tissue

May, D., Blow, M. J., Kaplan, T., McCulley, D. J., Jensen, B. C., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M. I., Wright, C., et al. (2011) · Nature Genetics · doi:10.1038/ng.1006 · Cited by 262 · see citing works

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

Junion, G., Spivakov, M., Girardot, C., Braun, M., Gustafson, E. H., Birney, E., & Furlong, E. E. M. (2012) · Cell · doi:10.1016/j.cell.2012.01.030 · Cited by 257 · see citing works

Plasmodium falciparum var gene expression is developmentally controlled at the level of RNA polymerase II‐mediated transcription initiation

Kyes, S., Christodoulou, Z., Pinches, R. A., Kriek, N., Horrocks, P., & Newbold, C. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05587.x · Cited by 257 · see citing works

Defining the Status of RNA Polymerase at Promoters

Core, L. J., Waterfall, J. J., Gilchrist, D. A., Fargo, D. C., Kwak, H., Adelman, K., & Lis, J. T. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.034 · Cited by 252 · see citing works

Gene regulation by nucleosome positioning

Bai, L., & Morozov, A. V. (2010) · Trends in Genetics · doi:10.1016/j.tig.2010.08.003 · Cited by 247 · see citing works

Enhancer Function: Mechanistic and Genome-Wide Insights Come Together

Plank, J. L., & Dean, A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.015 · Cited by 246 · see citing works

Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression

Vernimmen, D., Gobbi, M. D., Sloane‐Stanley, J. A., Wood, W. G., & Higgs, D. R. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601654 · Cited by 244 · see citing works

Gene Loops Enhance Transcriptional Directionality

Tan‐Wong, S. M., Zaugg, J. B., Camblong, J., Xu, Z., Zhang, D. W., Mischo, H. E., Ansari, A. Z., Luscombe, N. M., Steinmetz, L. M., & Proudfoot, N. J. (2012) · Science · doi:10.1126/science.1224350 · Cited by 241 · see citing works

Dynamics of Enhancer-Promoter Communication during Differentiation-Induced Gene Activation

Hatzis, P., & Talianidis, I. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00786-4 · Cited by 227 · see citing works

Wdr82 Is a C-Terminal Domain-Binding Protein That Recruits the Setd1A Histone H3-Lys4 Methyltransferase Complex to Transcription Start Sites of Transcribed Human Genes

Lee, J., & Skalnik, D. G. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01356-07 · Cited by 218 · see citing works

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

Moorman, C., Sun, L. V., Wang, J., de Wit, E., Talhout, W., Ward, L. D., Greil, F., Lu, X., White, K. P., Bussemaker, H. J., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605003103 · Cited by 211 · see citing works

Comparative analysis of regulatory information and circuits across distant species

Boyle, A. P., Araya, C. L., Brdlik, C. M., Cayting, P. D., Cheng, C., Cheng, Y., Gardner, K. E., Hillier, L., Janette, J., Jiang, L., et al. (2014) · Nature · doi:10.1038/nature13668 · Cited by 201 · see citing works

Maintaining Cell Identity through Global Control of Genomic Organization

Natoli, G. (2010) · Immunity · doi:10.1016/j.immuni.2010.07.006 · Cited by 199 · see citing works

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

Xu, J., Shao, Z., Glass, K., Bauer, D. E., Pinello, L., Handel, B. V., Hou, S., Stamatoyannopoulos, J. A., Mikkola, H. K. A., Yuan, G., et al. (2012) · Developmental Cell · doi:10.1016/j.devcel.2012.09.003 · Cited by 196 · see citing works

Transcription of the hypersensitive site HS2 enhancer in erythroid cells.

Tuan, D. Y. H., Kong, S., & Hu, K. Q. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.23.11219 · Cited by 196 · see citing works

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis -regulatory function of ChIP-seq peaks

White, M. A., Myers, C. A., Corbo, J. C., & Cohen, B. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307449110 · Cited by 195 · see citing works

Unamplified cap analysis of gene expression on a single-molecule sequencerPreprint

Kanamori-Katayama, M., Itoh, M., Kawaji, H., Lassmann, T., Katayama, S., Kojima, M., Bertin, N., Kaiho, A., Ninomiya, N., Daub, C. O., et al. (2011) · Genome Research · doi:10.1101/gr.115469.110 · Cited by 176 · see citing works

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

Kruesi, W. S., Core, L. J., Waters, C. T., Lis, J. T., & Meyer, B. J. (2013) · eLife · doi:10.7554/elife.00808 · Cited by 175 · see citing works

Enhancers and silencers: an integrated and simple model for their function

Kolovos, P., Knoch, T., Grosveld, F. G., Cook, P. R., & Papantonis, A. (2012) · Epigenetics & Chromatin · doi:10.1186/1756-8935-5-1 · Cited by 173 · see citing works

Insulators and promoters: closer than we think

Raab, J. R., & Kamakaka, R. T. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2765 · Cited by 171 · see citing works

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Andersson, R., Refsing Andersen, P., Valen, E., Core, L. J., Bornholdt, J., Boyd, M., Heick Jensen, T., & Sandelin, A. (2014) · Nature Communications · doi:10.1038/ncomms6336 · Cited by 171 · see citing works

Chromatin remodeling and extragenic transcription at the MHC class II locus control region

Masternak, K., Peyraud, N., Krawczyk, M., Barras, E., & Reith, W. (2003) · Nature Immunology · doi:10.1038/ni883 · Cited by 157 · see citing works

Comparative genomics of Drosophila and human core promoters

FitzGerald, P. C., Sturgill, D. M., Shyakhtenko, A., Oliver, B., & Vinson, C. (2006) · Genome biology · doi:10.1186/gb-2006-7-7-r53 · Cited by 154 · see citing works

HOT regions function as patterned developmental enhancers and have a distinct cis -regulatory signaturePreprint

Kvon, E. Z., Stampfel, G., Yáñez-Cuna, J. O., Dickson, B. J., & Stark, A. (2012) · Genes & Development · doi:10.1101/gad.188052.112 · Cited by 147 · see citing works

Widespread Misinterpretable ChIP-seq Bias in Yeast

Park, D., Lee, Y., Bhupindersingh, G., & Iyer, V. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083506 · Cited by 144 · see citing works

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

Fisher, W. W., Li, J. J., Hammonds, A. S., Brown, J. B., Pfeiffer, B. D., Weiszmann, R., MacArthur, S., Thomas, S., Stamatoyannopoulos, J. A., Eisen, M. B., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1209589110 · Cited by 140 · see citing works

Discovery of active enhancers through bidirectional expression of short transcripts

Melgar, M., Collins, F. S., & Sethupathy, P. (2011) · Genome biology · doi:10.1186/gb-2011-12-11-r113 · Cited by 136 · see citing works

Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patternsPreprint

Roh, T., Wei, G., Farrell, C. M., & Zhao, K. (2006) · Genome Research · doi:10.1101/gr.5767907 · Cited by 130 · see citing works

Transcription factories: genetic programming in three dimensions

Edelman, L. B., & Fraser, P. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.01.010 · Cited by 127 · see citing works

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

Wu, H., Nord, A. S., Akiyama, J. A., Shoukry, M. I., Afzal, V., Rubin, E. M., Pennacchio, L. A., & Visel, A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004610 · Cited by 125 · see citing works

Deciphering the transcriptional cis-regulatory code

Yáñez-Cuna, J. O., Kvon, E. Z., & Stark, A. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.09.007 · Cited by 124 · see citing works

A Survey of 6,300 Genomic Fragments for cis-Regulatory Activity in the Imaginal Discs of Drosophila melanogaster

Jory, A., Estella, C., Giorgianni, M. W., Slattery, M. G., Laverty, T., Rubin, G. M., & Mann, R. S. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.09.010 · Cited by 123 · see citing works

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

Paris, M., Kaplan, T., Li, X. Y., Villalta, J. E., Lott, S. E., & Eisen, M. B. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003748 · Cited by 90 · see citing works

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells

Philippakis, A., Busser, B. W., Gisselbrecht, S. S., He, F. S., Estrada, B., Michelson, A. M., & Bulyk, M. L. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020053 · Cited by 64 · see citing works

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

Gisselbrecht, S. S., Barrera, L. A., Porsch, M., Aboukhalil, A., Estep, P. W., Vedenko, A., Palagi, A., Kim, Y., Zhu, X., Busser, B. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2558 · Cited by 62 · see citing works

Initiating RNA Polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity

Koch, F., & Andrau, J. (2011) · Transcription · doi:10.4161/trns.2.6.18747 · Cited by 44 · see citing works

Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers, and Gene Bodies

Rajagopal, N., Ernst, J., Ray, P. R., Wu, J., Zhang, M. Q., Kellis, M., & Ren, B. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.013565 · Cited by 44 · see citing works

Uncoupling Transcription from Covalent Histone Modification

Zhang, H., Gao, L., Anandhakumar, J., & Gross, D. S. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004202 · Cited by 41 · see citing works

Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

Chen, Y., Jørgensen, M., Kolde, R., Zhao, X., Parker, B. J., Valen, E., Wen, J., & Sandelin, A. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-544 · Cited by 36 · see citing works

Developmental mechanisms and cis-regulatory codes

Ochoa‐Espinosa, A., & Small, S. (2006) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2006.02.014 · Cited by 26 · see citing works

Computational Identification of Active Enhancers in Model Organisms

Wang, C.-Q., Zhang, M. Q., & Zhang, Z.-H. (2013) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2013.04.002 · Cited by 23 · see citing works

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

Yokoyama, K. D., Zhang, Y., & Ma, J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003771 · Cited by 22 · see citing works

Eukaryotic core promoters and the functional basis of transcription initiation

Haberle, V., & Stark, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0028-8 · Cited by 737 · see citing works

Determinants of enhancer and promoter activities of regulatory elements

Andersson, R., & Sandelin, A. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0173-8 · Cited by 713 · see citing works

Membrane and Nuclear Estrogen Receptor Alpha Actions: From Tissue Specificity to Medical Implications

Arnal, J., Lenfant, F., Métivier, R., Flouriot, G., Henrion, D., Adlanmérini, M., Fontaine, C., Gourdy, P., Chambon, P., Katzenellenbogen, B. S., et al. (2017) · Physiological Reviews · doi:10.1152/physrev.00024.2016 · Cited by 428 · see citing works

The AP-1 transcriptional complex: Local switch or remote command?

Bejjani, F., Evanno, E., Zibara, K., Piechaczyk, M., & Jariel‐Encontre, I. (2019) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2019.04.003 · Cited by 355 · see citing works

Genome-wide characterization of mammalian promoters with distal enhancer functions

Dao, L. T. M., Galindo-Albarrán, A. O., Castro-Mondragon, J. A., Andrieu-Soler, C., Medina-Rivera, A., Souaid, C., Charbonnier, G., Griffon, A., Vanhille, L., Stephen, T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3884 · Cited by 281 · see citing works

Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors

Zabidi, M. A., & Stark, A. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.10.003 · Cited by 228 · see citing works

A unified architecture of transcriptional regulatory elements

Andersson, R., Sandelin, A., & Danko, C. G. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.05.007 · Cited by 211 · see citing works

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activationPreprint

Catarino, R. R., & Stark, A. (2018) · Genes & Development · doi:10.1101/gad.310367.117 · Cited by 205 · see citing works

The core promoter: At the heart of gene expression

Danino, Y. M., Even, D. Y., Ideses, D., & Juven‐Gershon, T. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.04.003 · Cited by 161 · see citing works

Genetic sources of population epigenomic variation

Taudt, A., Colomé‐Tatché, M., & Johannes, F. M. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.45 · Cited by 158 · see citing works

The Hierarchy of Transcriptional Activation: From Enhancer to Promoter

Vernimmen, D., & Bickmore, W. A. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.10.004 · Cited by 155 · see citing works

Genome-wide mapping of autonomous promoter activity in human cells

van Arensbergen, J., FitzPatrick, V. D., de Haas, M., Pagie, L., Sluimer, J., Bussemaker, H. J., & van Steensel, B. (2017) · Nature Biotechnology · doi:10.1038/nbt.3754 · Cited by 140 · see citing works

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificityPreprint

Mattioli, K., Volders, P.-J., Gerhardinger, C., Lee, J. C., Maass, P. G., Melé, M., & Rinn, J. L. (2019) · Genome Research · doi:10.1101/gr.242222.118 · Cited by 139 · see citing works

Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons

Scandaglia, M., López‐Atalaya, J. P., Medrano-Fernandez, A., López-Cascales, M. T., del Blanco, B., Lipiński, M., Benito, E., Olivares, R., Iwase, S., Shi, Y., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.09.014 · Cited by 123 · see citing works

In the loop: promoter–enhancer interactions and bioinformatics

Mora, A., Sandve, G. K., Gabrielsen, O. S., & Eskeland, R. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv097 · Cited by 115 · see citing works

Chromatin accessibility dynamics across C. elegans development and ageing

Jänes, J., Yan, D., Schoof, M., Serizay, J., Appert, A., Cerrato, C., Woodbury, C., Chen, R., Gemma, C., Huang, N., et al. (2018) · eLife · doi:10.7554/elife.37344 · Cited by 106 · see citing works

Transcription imparts architecture, function and logic to enhancer units

Tippens, N. D., Liang, J. H., Leung, A. K.-Y., Wierbowski, S. D., Ozer, A., Booth, J. G., Lis, J. T., & Yu, H. (2020) · Nature Genetics · doi:10.1038/s41588-020-0686-2 · Cited by 101 · see citing works

Why the activity of a gene depends on its neighbors

Feuerborn, A., & Cook, P. R. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.07.001 · Cited by 88 · see citing works

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

Zacher, B., Michel, M., Schwalb, B., Cramer, P., Tresch, A., & Gagneur, J. (2017) · PLOS ONE · doi:10.1371/journal.pone.0169249 · Cited by 91 · see citing works

Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases

Degtyareva, A. O., Antontseva, E. V., & Merkulova, T. I. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22126454 · Cited by 88 · see citing works

Functional Enhancers As Master Regulators of Tissue-Specific Gene Regulation and Cancer Development

Ko, J. Y., Oh, S., & Yoo, K. H. (2017) · Molecules and Cells · doi:10.14348/molcells.2017.0033 · Cited by 79 · see citing works

Widespread Enhancer Activity from Core Promoters

Medina-Rivera, A., Santiago-Algarra, D., Puthier, D., & Spicuglia, S. (2018) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2018.03.004 · Cited by 78 · see citing works

Enhancer RNA: What we know and what we can achieve

Han, Z., & Li, W. (2022) · Cell Proliferation · doi:10.1111/cpr.13202 · Cited by 74 · see citing works

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function

Benton, M. L., Talipineni, S. C., Kostka, D., & Capra, J. A. (2019) · BMC Genomics · doi:10.1186/s12864-019-5779-x · Cited by 68 · see citing works

Repurposing of promoters and enhancers during mammalian evolution

Carelli, F. N., Liechti, A., Halbert, J., Warnefors, M., & Kaessmann, H. (2018) · Nature Communications · doi:10.1038/s41467-018-06544-z · Cited by 66 · see citing works

Transcriptional regulation by promoters with enhancer function

Dao, L. T. M., & Spicuglia, S. (2018) · Transcription · doi:10.1080/21541264.2018.1486150 · Cited by 69 · see citing works

The identification of cis-regulatory elements: A review from a machine learning perspective

Li, Y., Chen, C., Kaye, A. M., & Wasserman, W. W. (2015) · Biosystems · doi:10.1016/j.biosystems.2015.10.002 · Cited by 65 · see citing works

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity

Pancaldi, V., Pau, E. C. D. S., Javierre, B. M., Juan, D., Fraser, P., Spivakov, M., Valencia, A., & Rico, D. (2016) · Genome biology · doi:10.1186/s13059-016-1003-3 · Cited by 64 · see citing works

Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers

Young, R. S., Kumar, Y., Bickmore, W. A., & Taylor, M. S. (2017) · Genome biology · doi:10.1186/s13059-017-1379-8 · Cited by 60 · see citing works

Recent advances in high-throughput approaches to dissect enhancer function

Santiago‐Algarra, D., Dao, L. T. M., Pradel, L. C., España, A. P., & Spicuglia, S. (2017) · F1000Research · doi:10.12688/f1000research.11581.1 · Cited by 56 · see citing works

Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers

Khan, A., Mathelier, A., & Zhang, X. (2018) · Epigenetics · doi:10.1080/15592294.2018.1514231 · Cited by 56 · see citing works

Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

Rennie, S., Dalby, M., Lloret-Llinares, M., Bakoulis, S., Vaagensø, C. D., Jensen, T. H., & Andersson, R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky244 · Cited by 53 · see citing works

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection

Wyler, E., Menegatti, J., Franke, V., Kocks, C., Boltengagen, A., Hennig, T., Theil, K., Rutkowski, A., Ferrai, C., Baer, L., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1329-5 · Cited by 40 · see citing works

Long-Range Control of V(D)J Recombination & Allelic Exclusion

Outters, P., Jaeger, S., Zaarour, N., & Ferrier, P. (2015) · Advances in immunology · doi:10.1016/bs.ai.2015.08.002 · Cited by 39 · see citing works

The origins of developmental gene regulation

Arenas‐Mena, C. (2017) · Evolution & Development · doi:10.1111/ede.12217 · Cited by 35 · see citing works

Probing transcription factor combinatorics in different promoter classes and in enhancers

Vandel, J., Cassan, O., Lèbre, S., Lecellier, C., & Bréhélin, L. (2019) · BMC Genomics · doi:10.1186/s12864-018-5408-0 · Cited by 35 · see citing works

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

Megraw, M. S., Cumbie, J. S., Ivanchenko, M. G., & Filichkin, S. A. (2016) · The Plant Cell · doi:10.1105/tpc.15.00852 · Cited by 33 · see citing works

AP-1 Signaling by Fra-1 Directly Regulates HMGA1 Oncogene Transcription in Triple-Negative Breast Cancers

Tolza, C., Bejjani, F., Evanno, E., Mahfoud, S., Moquet-Torcy, G., Gostan, T., Maqbool, M. A., Kirsh, O., Piechaczyk, M., & Jariel‐Encontre, I. (2019) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-19-0036 · Cited by 30 · see citing works

XRCC5 cooperates with p300 to promote cyclooxygenase-2 expression and tumor growth in colon cancers

Zhang, Z., Zheng, F., Yu, Z., Hao, J., Chen, M., Yu, W., Guo, W., Chen, Y., Huang, W., Duan, Z., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0186900 · Cited by 30 · see citing works

Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers

Steinhaus, R., Gonzalez, T., Seelow, D., & Robinson, P. N. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa223 · Cited by 28 · see citing works

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

Ren, C., Liu, F., Ouyang, Z., An, G., Zhao, C., Shuai, J., Cai, S., Bo, X., & Shu, W. (2017) · Scientific Reports · doi:10.1038/s41598-017-15822-7 · Cited by 28 · see citing works

Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality

Pundhir, S., Bagger, F. O., Lauridsen, F. B., Rapin, N., & Porse, B. T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw250 · Cited by 26 · see citing works

Changes Within H3K4me3-Marked Histone Reveal Molecular Background of Neutrophil Functional Plasticity

Piątek, P., Namiecińska, M., Lewkowicz, N., Michalska, M. K. , Jabłonowski, Z., Matysiak, M., Dulska, J., Michlewska, S., Wieczorek, M., & Lewkowicz, P. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.906311 · Cited by 23 · see citing works

Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework

Maeso, I., & Tena, J. J. (2015) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2015.12.003 · Cited by 22 · see citing works

Tissue-specific epigenetics in gene neighborhoods: myogenic transcription factor genes

Chandra, S., Terragni, J., Zhang, G., Pradhan, S., Haushka, S., Johnston, D. A., Baribault, C., Lacey, M. R., & Ehrlich, M. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv198 · Cited by 22 · see citing works

Genome-wide uniformity of human ‘open’ pre-initiation complexesPreprint

Lai, W., & Pugh, B. F. (2016) · Genome Research · doi:10.1101/gr.210955.116 · Cited by 20 · see citing works

TBX5-AS1, an enhancer RNA, is a potential novel prognostic biomarker for lung adenocarcinoma

Cheng, L., Han, T., Chen, B., Nie, K., & Peng, W. (2021) · BMC Cancer · doi:10.1186/s12885-021-08517-w · Cited by 19 · see citing works

Association of IL18 genetic polymorphisms with Chagas disease in Latin American populations

Strauss, M., Acosta‐Herrera, M., Alcaraz, A., Casares‐Marfil, D., Bosch‐Nicolau, P., Presti, M. S. L., Molina, I., González, C. I., Chagas Genetics CYTED Network, & Martín, J. (2019) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0007859 · Cited by 19 · see citing works

Selective phase separation of transcription factors is driven by orthogonal molecular grammar

Driver, M. D., & Onck, P. R. (2025) · Nature Communications · doi:10.1038/s41467-025-58445-7 · Cited by 18 · see citing works

Beyond modular enhancers: new questions in cis-regulatory evolution

McDonald, J. M. C., & Reed, R. D. (2024) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2024.07.005 · Cited by 15 · see citing works

Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity

Colbran, L. L., Chen, L., & Capra, J. (2019) · Genetics · doi:10.1534/genetics.118.301895 · Cited by 16 · see citing works

Short tandem repeats are important contributors to silencer elements in T cells

Hussain, S., Sadouni, N., van Essen, D., Dao, L. T. M., Ferré, Q., Charbonnier, G., Torres, M., Gallardo, F., Lecellier, C., Sexton, T., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad187 · Cited by 16 · see citing works

Intergenic and Intronic DNA Hypomethylated Regions as Putative Regulators of Imprinted Domains

Bakshi, A., Bretz, C. L., Cain, T. L., & Kim, J. (2018) · Epigenomics · doi:10.2217/epi-2017-0125 · Cited by 16 · see citing works

Enhancer Function in the 3D Genome

Razin, S. V., Ulianov, S. V., & Iarovaia, O. V. (2023) · Genes · doi:10.3390/genes14061277 · Cited by 15 · see citing works

A Glimpse to Background and Characteristics of Major Molecular Biological Networks

Altaf-Ul-Amin, M., Katsuragi, T., Sato, T., & Kanaya, S. (2015) · BioMed Research International · doi:10.1155/2015/540297 · Cited by 15 · see citing works

Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness

Gándara, L., Tsai, A., Ekelöf, M., Galupa, R., Noon, E. P., Alexandrov, T., & Crocker, J. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111832 · Cited by 14 · see citing works

Histone H3 posttranslational modified enzymes defined neutrophil plasticity and their vulnerability to IL-10 in the course of the inflammation

Piątek, P., Namiecińska, M., Lewkowicz, N., Michalska, M. K. , Jabłonowski, Z., Matysiak, M., Michlewska, S., Wieczorek, M., & Lewkowicz, P. (2024) · Journal of Inflammation · doi:10.1186/s12950-024-00389-8 · Cited by 12 · see citing works

High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range β-Globin Gene Regulation

Stees, J. R., Hossain, M. A., Sunose, T., Kudo, Y., Pardo, C. E., Nabilsi, N. H., Darst, R. P., Poudyal, R., Igarashi, K., Huang, S., et al. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00723-15 · Cited by 11 · see citing works

Heterogeneity among enhancer RNAs: origins, consequences and perspectives

Syed, K. M., & Hon, C.-C. (2021) · Essays in Biochemistry · doi:10.1042/ebc20200064 · Cited by 11 · see citing works

Predicted deleterious mutations reveal the genetic architecture of male reproductive success in a lekking bird

Chen, R. S., Soulsbury, C. D., Hench, K., van Oers, K., & Hoffman, J. I. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02802-8 · Cited by 12 · see citing works

Contribution of spurious transcription to intellectual disability disorders

Scandaglia, M., & Barco, Á. (2019) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2018-105668 · Cited by 11 · see citing works

Bioinformatics approaches to predict target genes from transcription factor binding data.

Essebier, A., Lamprecht, M. L., Piper, M., & Bodén, M. (2017) · Methods · doi:10.1016/j.ymeth.2017.09.001 · Cited by 10 · see citing works

Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing

Lee, C., Wang, K., Qin, T., & Sartor, M. A. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00199 · Cited by 8 · see citing works

Analysis of the landscape of human enhancer sequences in biological databases

Mulero-Hernández, J., & Fernández‐Breis, J. T. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.045 · Cited by 7 · see citing works

Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrity

Sun, C., Ruzycki, P. A., & Chen, S. (2023) · Scientific Reports · doi:10.1038/s41598-023-39979-6 · Cited by 6 · see citing works

Current Status of Genomic Maps: Genomic Selection/GBV in Livestock

Blasco, A., & Pena, R. N. (2018) · Springer eBooks · doi:10.1007/978-3-319-92348-2_4 · Cited by 6 · see citing works

Transcription Factor SP2 Regulates Ski-mediated Astrocyte Proliferation In Vitro

Da, C.-M., Liao, H.-Y., Deng, Y., Zhao, G., Ma, L., & Zhang, H. (2021) · Neuroscience · doi:10.1016/j.neuroscience.2021.10.013 · Cited by 6 · see citing works

MiR-4732-3p Prevents Lung Cancer Progression via Inhibition of the TBX15/TNFSF11 Axis

Li, P., Li, Y., Bai, S., Zhang, Y., & Zhao, L. (2023) · Epigenomics · doi:10.2217/epi-2023-0009 · Cited by 6 · see citing works

Liver kinase B1 ( LKB1 ) regulates the epigenetic landscape of mouse pancreatic beta cells

Haberman, N., Cheung, R., Pizza, G., Cvetešić, N., Nagy, D., Maude, H., Blázquez, L., Lenhard, B., Cebola, I., Rutter, G. A., et al. (2024) · The FASEB Journal · doi:10.1096/fj.202401078r · Cited by 4 · see citing works

Current progress and future perspective of super-enhancers: a viable and effective bridge between the transcriptional apparatus and disease

Wang, R., Li, A., & Pang, Z. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1611905 · Cited by 4 · see citing works

Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes

Malfait, J., Wan, J., Singh, H. N., Souaid, C., Farah, G., Su, J., Torres, M., Manosalva, I., Sakakini, N., Esnault, C., et al. (2026) · The EMBO Journal · doi:10.1038/s44318-025-00670-3 · Cited by 4 · see citing works

Approches haut débit pour l’étude des séquences cis-régulatrices

España, A. P., Santiago‐Algarra, D., Pradel, L. C., & Spicuglia, S. (2017) · Biologie Aujourd hui · doi:10.1051/jbio/2018015 · Cited by 4 · see citing works

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing

Ho, E. Y.-K., Cao, Q., Gu, M., Chan, R. W.-L., Wu, Q., Gerstein, M., & Yip, K. Y.-L. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz030 · Cited by 4 · see citing works

Probing transcription factor combinatorics in different promoter classes and in enhancersPreprint

Vandel, J., Cassan, O., Lèbre, S., Lecellier, C., & Bréhélin, L. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/197418 · Cited by 4 · see citing works

Identifying promoter and enhancer sequences by graph convolutional networks

Tenekeci, S., & Tekır, S. (2024) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2024.108040 · Cited by 3 · see citing works

Full-length mRNA sequencing resolves novel variation in 5′ UTR length for genes expressed during human CD4 T-cell activation

Woolley, C. R., Chariker, J. H., Rouchka, E. C., Ford, E. E., Hudson, E., Rasche, K. M., Whitley, C. S., Vanwinkle, Z. M., Casella, C. R., Smith, M. L., et al. (2025) · Immunogenetics · doi:10.1007/s00251-025-01371-1 · Cited by 4 · see citing works

Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish

Trinh, L. A., Chong-Morrison, V., & Sauka‐Spengler, T. (2018) · Methods · doi:10.1016/j.ymeth.2018.07.011 · Cited by 3 · see citing works

Chromatin accessibility is dynamically regulated across C. elegans development and ageingPreprint

Jänes, J., Dong, Y., Schoof, M., Serizay, J., Appert, A., Cerrato, C., Woodbury, C., Chen, R., Gemma, C., Huang, N., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/279158 · Cited by 3 · see citing works

Mapping Regulatory Elements within 5' and 3' UTRs of SIGLEC15 with a Use of Reporter System

Wang, L., Li, R., Lai, X., Zhang, X., Chen, H., & Zhao, W. (2022) · Molecular Biology · doi:10.1134/s0026893322030141 · Cited by 2 · see citing works

Downregulation of enhancer RNA AC003092.1 is associated with poor prognosis in kidney renal clear cell carcinoma

Li, J., Gan, J., Chen, C., Yuan, Y., Xiong, X., Li, L., Luo, P., & Zhang, W. (2024) · Scientific Reports · doi:10.1038/s41598-024-64431-8 · Cited by 2 · see citing works

Enhancer‐dependent gene regulation in space, time, and malignancies

Blum, B., Dachtler, V., & Feldmann, A. (2025) · International Journal of Cancer · doi:10.1002/ijc.35350 · Cited by 2 · see citing works

The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes

Rastegar, S., & Strähle, U. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2016.04.003 · Cited by 2 · see citing works

Role of SLC44A3-AS1 Enhancer RNA in Esophageal Cancer Prognosis

Kang, K., Wu, J., Mao, Y., Kai, J., Chen, S., & Xiong, F. (2023) · Journal of College of Physicians And Surgeons Pakistan · doi:10.29271/jcpsp.2023.09.964 · Cited by 1 · see citing works

Cooperativity between regulatory elements acts as a modulator of enhancer function

Balasubramanian, D., Masoura, M., & Ghavi-Helm, Y. (2026) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102427 · Cited by 1 · see citing works

Enhancer RNAs: similarities with both lncRNAs and mRNAs reveal novel functions

Vlasov, P. A., & Manley, J. L. (2026) · RNA Biology · doi:10.1080/15476286.2026.2682066 · Cited by 1 · see citing works

Parsing the stepwise molecular evolution of C4-associated β -carbonic anhydrase in the genus Flaveria

Baros, C. J., Saladié, M., Beerkens, J., Cohen, J. B., Ng, J. E., Waters, M. T., & Ludwig, M. L. (2026) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiag368 · Cited by 1 · see citing works

Genome-wide active enhancer identification using cell type-specific signatures of epigenomic activityPreprint

Jhanwar, S., Ossowski, S., & Dávila-Velderrain, J. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/421230 · Cited by 1 · see citing works

High-throughput functional analysis of IncRNA core promoters elucidatesrules governing tissue-specificityPreprint

Mattioli, K., Volders, P.-J., Gerhardinger, C., Lee, J. C., Maass, P. G., Melé, M., & Rinn, J. L. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/482232 · Cited by 1 · see citing works

Accurate transcription start sites enable mining for the cis-regulatory determinants of tissue specific gene expressionPreprint

Ansariola, M., Fraser, V. N., Filichkin, S. A., Ivanchenko, M. G., Bright, Z. A., Gould, R. A., Ozguc, O. R., O’Neil, S. T., & Megraw, M. S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.01.278424 · Cited by 1 · see citing works

Chromatin accessibility is dynamically regulated across C. elegans development and ageingPreprint

Jänes, J., Dong, Y., Schoof, M., Serizay, J., Appert, A., Cerrato, C., Woodbury, C., Chen, R., Gemma, C., Huang, N., et al. (2018) · MDC Repository (Max-Delbrueck-Center for Molecular Medicine) · Cited by 2 · see citing works

Developmental phenomics suggests that H3K4 monomethylation catalyzed by Trr functions as a phenotypic capacitorPreprint

Gándara, L., Tsai, A., Ekelöf, M., Galupa, R., Noon, E. P., Alexandrov, T., & Crocker, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.15.484407 · Cited by 1 · see citing works

Hand2 represses non-cardiac cell fates through chromatin remodeling at cis- regulatory elementsPreprint

Komatsu, V., Cooper, B. H., Yim, P., Chan, K., Gong, W., Wheatley, L., Rohs, R., Fraser, S. E., & Trinh, L. A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.23.559156 · Cited by 1 · see citing works

Chromatin assortativity: Integrating epigenomic data and 3D genomic structurePreprint

Pancaldi, V., Pau, E. C. D. S., Javierre, B. M., Juan, D., Fraser, P., Spivakov, M., Valencia, A., & Rico, D. (2015) · arXiv (Cornell University)

Avaliação do controle da expressão gênica de citocinas pró inflamatórias mediado pela IL-10. Participação da IL-10 na modulação da resposta inflamatória exercida pela glutamina e na restrição alimentar

de Oliveira, D. C. (2017) · doi:10.11606/t.9.2017.tde-16112017-174159

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativityPreprint

Pancaldi, V., Pau, E. C. D. S., Javierre, B. M., Juan, D., Fraser, P., Spivakov, M., Valencia, A., & Rico, D. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1512.00268

TBX5-AS1, an enhancer RNA, is a potential novel prognostic biomarker for lung adenocarcinomaPreprint

Cheng, L., Han, T., Chen, B., Nie, K., & Peng, W. (2021) · Research Square · doi:10.21203/rs.3.rs-386241/v1

Faculty Opinions recommendation of Transcription imparts architecture, function and logic to enhancer units.

Sharrocks, A. D. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738702238.793579142

Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrityPreprint

Sun, C., Ruzycki, P. A., & Chen, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.02.518920

Aktueller Stand der genomischen Karten: Genomische Selektion/GBV bei Nutztieren

Blasco, A., & Pena, R. N. (2023) · Springer eBooks · doi:10.1007/978-3-031-26042-1_4

Downregulation of enhancer RNA AC003092.1 is associated with poor prognosis in kidney renal clear cell carcinomaPreprint

Chen, C., Li, L., Xiong, X., Yuan, Y., Yang, J. J. J., Luo, P., & Zhang, W. (2023) · Research Square · doi:10.21203/rs.3.rs-3360211/v1

Determinants of enhancer and promoter activities of regulatory elements

Andersson, R., & Sandelin, A. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0173-8 · Cited by 713 · see citing works

A unified architecture of transcriptional regulatory elements

Andersson, R., Sandelin, A., & Danko, C. G. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.05.007 · Cited by 211 · see citing works

Evaluating Enhancer Function and Transcription

Field, A. R., & Adelman, K. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-011420-095916 · Cited by 218 · see citing works

High-throughput functional comparison of promoter and enhancer activities

Nguyen, T. A., Jones, R. D., Snavely, A. R., Pfenning, A. R., Kirchner, R., Hemberg, M., & Gray, J. M. (2016) · Genome Research · doi:10.1101/gr.204834.116 · Cited by 146 · see citing works

Architectural and Functional Commonalities between Enhancers and Promoters

Kim, T.-K., & Shiekhattar, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.008 · Cited by 331 · see citing works